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Nacho Molina

@molinalab.bsky.social
1.7K followers 1.2K following 112 posts

Group leader of the Stochastic Systems Biology Lab at IGBMC - CNRS - University of Strasbourg. Models of gene regulation based on biophysics-informed deep learning: www.igbmc.fr/molina

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Nacho Molina @molinalab.bsky.social · 03/10/2026
It was a pleasure to collaborate on this beautiful piece of work led by Susan Mango: nature.com/articles/s41...
nature.com
Single-molecule chromatin tracing reveals a diversity of megabase heterochromatin domains - Nature Structural & Molecular Biology
Single-molecule imaging reveals diverse, megabase-scale heterochromatin domains in C. elegans. Some resemble TADs and depend on condensin I; others are independent of condensin and histone H3K9me, inc...
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Nacho Molina @molinalab.bsky.social · 24/09/2026
Interested in #CellCycle and #Pluripotency? 👇
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Tineke Lenstra @tinekelenstra.bsky.social · 17/08/2026
Sign up now for the EMBO meeting 'quantitative biology to molecular mechanisms'. Fantastic speaker lineup and plenty of speakers slots selected from abstracts. Submit your abstract before Sept 11!
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Nacho Molina @molinalab.bsky.social · 24/09/2026
And finally! We produced a scRNA-seq time course of hiPSCs differentiating into definitive endoderm, and we found that lineage commitment remodels the cell cycle in a coordinated way.
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Nacho Molina @molinalab.bsky.social · 24/09/2026
Surprisingly (at least to us), mRNA degradation timing is more conserved than transcriptional timing. The phase at which genes reach peak degradation correlates across organisms more strongly than the phase of peak transcription. #RNAkinetics, #PosttranscriptionalRegulation
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Nacho Molina @molinalab.bsky.social · 24/09/2026
We have developed Ciclopes, a biology-informed deep-learning framework that uses an autoencoder to reconstruct periodic gene expression dynamics and estimates phase-dependent transcription and degradation rates #CompBio, #DeepLearning, #MechansticModelling, #scRNAseq.
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Nacho Molina @molinalab.bsky.social · 24/09/2026
We found that mouse and human use distinct regulatory regimes for cell-cycle control. Mouse pluripotent systems keep a higher baseline expression of core cell-cycle regulators, whereas human systems show larger oscillatory amplitude with a lower baseline. #Pluripotency #CellCycle
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Nacho Molina @molinalab.bsky.social · 24/09/2026
@maulik_nariya took single-cell RNA sequencing data from 6 human and mouse pluripotent systems spanning different naïve and primed states and culture conditions and estimated a continuous cell-cycle phase for each cell, leading to periodic gene expression dynamics.
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Nacho Molina @molinalab.bsky.social · 24/09/2026
Hey! You can have a look at our new preprint on #CellCycle regulation and #Pluripotency! A little thread 100% human 0% AI slop is coming (bear with me the mistakes). Let's thank first @maulik_nariya, the fantastic postdoc that led this project: www.biorxiv.org/content/10.6...
biorxiv.org
Comparison of cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems
Cell-cycle remodeling is fundamental to pluripotency and lineage commitment, yet whether its transcriptional and post-transcriptional architecture is conserved across species and developmental states ...
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Nacho Molina @molinalab.bsky.social · 15/06/2026
With a bit of delay, I am very happy to share that after more than 20 years building my scientific career across Europe, I have returned to my hometown, Madrid, as Full Professor at IE University. An exciting new step and much to build ahead. More here: www.linkedin.com/feed/update/...
linkedin.com
With a bit of delay, I am delighted to share that I have started a new position as Full Professor at IE University. After more than 20 years building my scientific career across Europe, it is very… |...
With a bit of delay, I am delighted to share that I have started a new position as Full Professor at IE University. After more than 20 years building my scientific career across Europe, it is very sp...
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Samuel Zambrano @samuzambrano.bsky.social · 26/02/2026
So grateful to my buddy the great @davidemazza.bsky.social and all the contributors from our teams to this joint effort to unravel NF-κB–p53 crosstalk. Davide’s thread nicely explains the main findings — here’s a short side note from me 🧵👇 (1/n)
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László Tora @tlaszlo.bsky.social · 24/12/2025
Read our new preprint where we uncover a hierarchy in human PIC assembly and establish a quantitative framework that connects factor exchange kinetics to the regulation of Pol II activity in living human cells. doi: doi.org/10.64898/202... By A. Oravecz and our collaborators @molinalab.bsky.social
doi.org
RNA polymerase II initiation factors show different dynamic behaviour upon induced transcription in live cells
Transcription by RNA polymerase II (Pol II) requires the ordered action of general transcription factors (GTFs) forming the pre-initiation complex (PIC). How these events unfold kinetically remains un...
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Nacho Molina @molinalab.bsky.social · 21/08/2025
Congratulations, Arnaud!
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Arnaud Krebs @arnaudkr.bsky.social · 18/08/2025
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
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kasitc.bsky.social @kasitc.bsky.social · 18/08/2025
Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...
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Schubeler Lab @schubelerlab.bsky.social · 07/08/2025
Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....
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Yad Ghavi-Helm @yghavi.bsky.social · 23/07/2025
Now available in its final form @narjournal.bsky.social ! doi.org/10.1093/nar/... Find out how we can reconstruct enhancer activity in vivo in the Drosophila embryo using scRNAseq data and Optimal Transport.
doi.org
Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms
Abstract. Enhancers play an essential role in developmental processes by regulating the spatiotemporal expression of genes. Characterizing their spatiotemp
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Arnaud Krebs @arnaudkr.bsky.social · 18/07/2025
#EMBLsinglemolecule was a blast! Happy to host the birth of single molecule genomics as a field and to think about the future with the microscopy crowd. Thanks to participants and organizers!
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EMBL Events @events.embl.org · 17/07/2025
Carrying on with Session 4 on #EMBLSingleMolecule Day 3 🤓💪🏼 ➡️ 'Decoding Gene Regulation at the Single-Molecule Level through Biophysical Modeling of DNA Footprinting Data' 🎙️ Nacho Molina – Institute of Genetics and Molecular and Cellular Biology @molinalab.bsky.social @igbmc.bsky.social @embl.org
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Slavov Laboratory @slavovlab.bsky.social · 11/06/2025
The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube: 𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧 youtu.be/adkY6txDyqs?...
youtu.be
Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025
YouTube video by Nikolai Slavov
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Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 03/06/2025
🚨 Only a few more days to REGISTER for the TriRhena Gene Regulation Club in Freiburg. Whether you are new or an established researcher in the Basel-Freiburg-Strasbourg region, this is your meeting when working in transcription, chromatin & gene regulation! ✍️ www.ie-freiburg.mpg.de/gene-regulat...
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Nikolai Slavov @slavov-n.bsky.social · 31/05/2025
🟦 Label-free single-cell proteomics (blue bars). 🟧 Multiplexed single-cell proteomics affords higher throughput (orange bars). ⬛️ Proteome depth & quantitative accuracy are comparable. We aim to make the 🟧 bars taller. www.parallelsq.org/psmtags www.biorxiv.org/content/10.1...
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Nacho Molina @molinalab.bsky.social · 29/05/2025
For Spanish speakers, this is a fantastic podcast about science and much more!
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Nacho Molina @molinalab.bsky.social · 28/05/2025
No doubt, this is one of the most exciting meetings of the year! And we will present our new method, HiddenFoot 😉: www.biorxiv.org/content/10.1...
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EMBL Events @events.embl.org · 27/05/2025
‼️Last chance to join us in person for #EMBLSingleMolecule! Attend talks, network, socialise, and experience the atmosphere on the campus 🤩 🎫 Register by 3 Jun 👉🏼 s.embl.org/grg25-01-bl 🧬RNA processing 🧬Translation 🧬Transcription & chromatin regulation 🧬Method development 🧬Theory
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Nacho Molina @molinalab.bsky.social · 22/05/2025
Very cool, Lars! Congrats!
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Lars Velten @larsplus.bsky.social · 21/05/2025
Out @nature.com: Clonal tracing with somatic epimutations 🧬 Single cell methylome encodes cell state & clonal identity 🔨 EPI-Clone reads out both (+mutations, +RNA) at scale 🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations doi.org/10.1038/s415... 🧵
doi.org
Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature
The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...
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Nacho Molina @molinalab.bsky.social · 21/05/2025
Just in case you missed this and it’s something that might interest you. #SingleMoleculeBiology, #Chromatin, #Transcription, #TF, #Nucleosome, #PolII, #Biophysics, #MachineLearning, #ComputationalBiology 👇
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Nacho Molina @molinalab.bsky.social · 19/05/2025
Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6
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Nacho Molina @molinalab.bsky.social · 20/05/2025
Thanks!
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Selin Jessa @selinjessa.com · 03/05/2025
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
biorxiv.org
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
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Nacho Molina @molinalab.bsky.social · 19/05/2025
Thanks!
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Dr Zeinab Rekad 🔬🧬🧪 @zeinabrekad.bsky.social · 19/05/2025
I'm neighboring the chromatin biology field at the moment and there is a lot I need to understand. Especially, the specific techniques/methodologies in use to study chromatin, however this one looks 🔥🔥🔥. Many congratulations 👏🏻 🎉 to all those involved! Hey #ChromatinSky people where are you at 🤩?
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Nacho Molina @molinalab.bsky.social · 19/05/2025
media.tenor.com
a man with long hair and a mustache is wearing a pink unicorn shirt
ALT: a man with long hair and a mustache is wearing a pink unicorn shirt
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Nacho Molina @molinalab.bsky.social · 19/05/2025
Muchas gracias!!!
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Nacho Molina @molinalab.bsky.social · 19/05/2025
Finally, if you've made it this far, you might be interested in testing the code. Feedback is very welcome! github.com/MolinaLab-IG... 6/6
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Nacho Molina @molinalab.bsky.social · 19/05/2025
HiddenFoot also works with Fiber-seq data! It reveals chromatin structure and nucleosome occupancy heterogeneity at single-molecule resolution driven by TF binding. 5/6
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Nacho Molina @molinalab.bsky.social · 19/05/2025
HiddenFoot resolves Pol II and nucleosome occupancy at the HIV-1 promoter, molecule by molecule. Under transcriptional inhibition (TLD), Pol II footprints vanish, while nucleosome occupancy at the +1 and −1 positions increases. 4/6
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Nacho Molina @molinalab.bsky.social · 19/05/2025
HiddenFoot infers pairwise interaction energies from single-molecule data and compares them to simulated equilibrium profiles to distinguish true TF–TF cooperativity from nucleosome-mediated co-binding. 3/6
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Nacho Molina @molinalab.bsky.social · 19/05/2025
HiddenFoot is a thermodynamics-based model that integrates known TF PWMs and nucleosome occupancy to efficiently evaluate all possible non-overlapping binding configurations. It fits model parameters using both stochastic gradient descent and MCMC. 2/6
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Nacho Molina @molinalab.bsky.social · 19/05/2025
Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6
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Nacho Molina @molinalab.bsky.social · 17/05/2025
🚨 New preprint out! Do you think Single Molecule Footprinting and Fiber-seq are super cool but aren't sure how to unlock their full potential? HiddenFoot can help you: www.biorxiv.org/content/10.1...
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Erik van Nimwegen @erikvannimwegen.bsky.social · 09/05/2025
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
biorxiv.org
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
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Molecular Systems Biology @molsystbiol.org · 08/05/2025
New research by @kasitc.bsky.social @molinalab.bsky.social @arnaudkr.bsky.social reveals limited RNA polymerase II pausing at mouse promoters compared to flies ➡️ www.embopress.org/doi/full/10....
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Manuel Mendoza @longchrom.bsky.social · 30/04/2025
US colleagues: Looking to launch or move your lab to France? The ARC Foundation is recruiting outstanding US-based scientists to lead research in oncology. Generous support & relocation help included. Details here: www.fondation-arc.org/projets/recr... Interested? Contact us!
fondation-arc.org
Recruiting international leaders in oncology from USA 2025
By offering a significant support, the call for proposal "Recruiting international leaders in Oncology from USA" wishes to allow the implantation in France of new scientific leader that will establish...
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ME Torres-Padilla @metorrespadilla.bsky.social · 23/04/2025
Here is-🥳🥳😇 tremendous effort by @palmrinmoy.bsky.social brilliantly supported by @tamas-schauer.bsky.social &super help by federico,iliya,tsune,adam,@mamartirenom.bsky.social Very happy to see this come to fruition- Look forward to feedback from colleagues ! More 👉 www.cell.com/cell/fulltex...
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Gradwohl Gérard @pancint.bsky.social · 17/04/2025
1/2. I am pleased to announce that the preprint of our latest study characterizing mouse and human EEC development is now on BioRxiv. A great collaboration with the @molinalab.bsky.social and Maxime Mahe (not on bluesky) www.biorxiv.org/cgi/content/...
biorxiv.org
Unraveling Enteroendocrine Cell lineage dynamics and associated gene regulatory networks during intestinal development
Enteroendocrine cells (EECs) are rare intestinal epithelial cells producing multiple hormones that regulate essential aspects of digestion and energy. EEC subtypes, their hormone repertoire and differ...
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Arnaud Krebs @arnaudkr.bsky.social · 10/04/2025
Send us your abstract before easter! Extended deadline! we got lots of cool stories already! We would also welcome submissions with a focus on Translation and life of RNA!
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Manuel Mendoza @longchrom.bsky.social · 09/04/2025
🚨3 weeks left to apply!🚨 We’re hiring 2 new Group Leaders at IGBMC – early career researchers welcome 🌟 We offer salary support for up to 3 years while you secure a permanent position in the French system. Come join an international research environment in Strasbourg! www.nature.com/naturecareer...
nature.com
Call For Two Group Leader Positions - Strasbourg-Ville, Bas-Rhin (FR) job with IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) | 12837602
The Institute of Genetics, Molecular and Cellular Biology (IGBMC) is seeking two outstanding group leaders to establish independent research teams.
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EMBL Events @events.embl.org · 01/04/2025
🚨 Last chance to submit abstract for 'Gene regulation: one molecule at a time' 🧬✍🏼 👉🏼 s.embl.org/grg25-01-bl ℹ️ #EMBLSingleMolecule will catalyse the emergence of a new generation of mechanistic models of the regulation of genes across each steps of the central dogma. 📅 Deadline: 8 April!
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